diff --git a/extensions/ql-vscode/src/config.ts b/extensions/ql-vscode/src/config.ts
index 3a6f002c5..2b7607f8a 100644
--- a/extensions/ql-vscode/src/config.ts
+++ b/extensions/ql-vscode/src/config.ts
@@ -670,7 +670,7 @@ export function getQlPackLocation(): string | undefined {
 }
 
 export async function setQlPackLocation(folder: string | undefined) {
-  await QL_PACK_LOCATION.updateValue(folder, ConfigurationTarget.Global);
+  await QL_PACK_LOCATION.updateValue(folder, ConfigurationTarget.Workspace);
 }
 
 /**
@@ -690,7 +690,10 @@ export function getAutogenerateQlPacks(): AutogenerateQLPacks {
 }
 
 export async function setAutogenerateQlPacks(choice: AutogenerateQLPacks) {
-  await AUTOGENERATE_QL_PACKS.updateValue(choice, ConfigurationTarget.Global);
+  await AUTOGENERATE_QL_PACKS.updateValue(
+    choice,
+    ConfigurationTarget.Workspace,
+  );
 }
 
 /**
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/local-queries/skeleton-query-wizard.test.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/local-queries/skeleton-query-wizard.test.ts
index 2347eb814..3182d7310 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/local-queries/skeleton-query-wizard.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/local-queries/skeleton-query-wizard.test.ts
@@ -399,7 +399,7 @@ describe("SkeletonQueryWizard", () => {
 
       await wizard.determineStoragePath();
 
-      expect(updateValueSpy).toHaveBeenCalledWith(storagePath, 1);
+      expect(updateValueSpy).toHaveBeenCalledWith(storagePath, 2);
     });
 
     describe("when the user is using the codespace template", () => {
diff --git a/extensions/ql-vscode/test/vscode-tests/minimal-workspace/local-queries/local-databases.test.ts b/extensions/ql-vscode/test/vscode-tests/minimal-workspace/local-queries/local-databases.test.ts
index 63a3d47ee..d24cb4b60 100644
--- a/extensions/ql-vscode/test/vscode-tests/minimal-workspace/local-queries/local-databases.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/minimal-workspace/local-queries/local-databases.test.ts
@@ -628,7 +628,7 @@ describe("local databases", () => {
         await (databaseManager as any).createSkeletonPacks(mockDbItem);
 
         expect(generateSpy).not.toBeCalled();
-        expect(updateValueSpy).toHaveBeenCalledWith("never", 1);
+        expect(updateValueSpy).toHaveBeenCalledWith("never", 2);
       });
 
       it("should create the skeleton QL pack for the user", async () => {